diff --git a/README.md b/README.md
new file mode 100644
index 0000000..b17ce7b
--- /dev/null
+++ b/README.md
@@ -0,0 +1,8 @@
+
+# BIO00088H-data
+
+<!-- badges: start -->
+<!-- badges: end -->
+
+The goal of BIO00088H-data is to ...
+
diff --git a/_site/omics/week-3/study_before_workshop.html b/_site/omics/week-3/study_before_workshop.html
index 2c1f1d3..5bee2fb 100644
--- a/_site/omics/week-3/study_before_workshop.html
+++ b/_site/omics/week-3/study_before_workshop.html
@@ -53,6 +53,8 @@
   <link href="../../site_libs/revealjs/plugin/quarto-line-highlight/line-highlight.css" rel="stylesheet">
   <link href="../../site_libs/revealjs/plugin/reveal-menu/menu.css" rel="stylesheet">
   <link href="../../site_libs/revealjs/plugin/reveal-menu/quarto-menu.css" rel="stylesheet">
+  <link href="../../site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/css/all.css" rel="stylesheet">
+  <link href="../../site_libs/revealjs/plugin/reveal-chalkboard/style.css" rel="stylesheet">
   <link href="../../site_libs/revealjs/plugin/quarto-support/footer.css" rel="stylesheet">
   <style type="text/css">
 
@@ -355,7 +357,7 @@ <h1 class="title">Independent Study to prepare for workshop</h1>
 </div>
 </div>
 
-  <p class="date">13 September, 2023</p>
+  <p class="date">1 October, 2023</p>
 </section>
 <section id="omics-workshops" class="slide level2">
 <h2>Omics workshops</h2>
@@ -505,7 +507,7 @@ <h2>Deliverables</h2>
 </ol>
 
 <div class="footer footer-default">
-
+<p>🔗 <a href="https://3mmarand.github.io/BIO00088H-data/omics/week-3/overview.html">About Omics 1: Hello data!</a></p>
 </div>
 <div id="refs" class="references csl-bib-body hanging-indent" role="list">
 <div id="ref-nestorowa2016" class="csl-entry" role="listitem">
@@ -523,6 +525,7 @@ <h2>Deliverables</h2>
   <script src="../../site_libs/revealjs/plugin/pdf-export/pdfexport.js"></script>
   <script src="../../site_libs/revealjs/plugin/reveal-menu/menu.js"></script>
   <script src="../../site_libs/revealjs/plugin/reveal-menu/quarto-menu.js"></script>
+  <script src="../../site_libs/revealjs/plugin/reveal-chalkboard/plugin.js"></script>
   <script src="../../site_libs/revealjs/plugin/quarto-support/support.js"></script>
   
 
@@ -544,7 +547,8 @@ <h2>Deliverables</h2>
 'autoAnimateEasing': "ease",
 'autoAnimateDuration': 1,
 'autoAnimateUnmatched': true,
-'menu': {"side":"left","useTextContentForMissingTitles":true,"markers":false,"loadIcons":false,"custom":[{"title":"Tools","icon":"<i class=\"fas fa-gear\"></i>","content":"<ul class=\"slide-menu-items\">\n<li class=\"slide-tool-item active\" data-item=\"0\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.fullscreen(event)\"><kbd>f</kbd> Fullscreen</a></li>\n<li class=\"slide-tool-item\" data-item=\"1\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.speakerMode(event)\"><kbd>s</kbd> Speaker View</a></li>\n<li class=\"slide-tool-item\" data-item=\"2\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.overview(event)\"><kbd>o</kbd> Slide Overview</a></li>\n<li class=\"slide-tool-item\" data-item=\"3\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.togglePdfExport(event)\"><kbd>e</kbd> PDF Export Mode</a></li>\n<li class=\"slide-tool-item\" data-item=\"4\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.keyboardHelp(event)\"><kbd>?</kbd> Keyboard Help</a></li>\n</ul>"}],"openButton":true},
+'menu': {"side":"left","useTextContentForMissingTitles":true,"markers":false,"loadIcons":false,"custom":[{"title":"Tools","icon":"<i class=\"fas fa-gear\"></i>","content":"<ul class=\"slide-menu-items\">\n<li class=\"slide-tool-item active\" data-item=\"0\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.fullscreen(event)\"><kbd>f</kbd> Fullscreen</a></li>\n<li class=\"slide-tool-item\" data-item=\"1\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.speakerMode(event)\"><kbd>s</kbd> Speaker View</a></li>\n<li class=\"slide-tool-item\" data-item=\"2\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.overview(event)\"><kbd>o</kbd> Slide Overview</a></li>\n<li class=\"slide-tool-item\" data-item=\"3\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.togglePdfExport(event)\"><kbd>e</kbd> PDF Export Mode</a></li>\n<li class=\"slide-tool-item\" data-item=\"4\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.toggleChalkboard(event)\"><kbd>b</kbd> Toggle Chalkboard</a></li>\n<li class=\"slide-tool-item\" data-item=\"5\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.toggleNotesCanvas(event)\"><kbd>c</kbd> Toggle Notes Canvas</a></li>\n<li class=\"slide-tool-item\" data-item=\"6\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.downloadDrawings(event)\"><kbd>d</kbd> Download Drawings</a></li>\n<li class=\"slide-tool-item\" data-item=\"7\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.keyboardHelp(event)\"><kbd>?</kbd> Keyboard Help</a></li>\n</ul>"}],"openButton":true},
+'chalkboard': {"buttons":true},
 'smaller': false,
  
         // Display controls in the bottom right corner
@@ -565,7 +569,7 @@ <h2>Deliverables</h2>
         progress: true,
 
         // Display the page number of the current slide
-        slideNumber: false,
+        slideNumber: 'c/t',
 
         // 'all', 'print', or 'speaker'
         showSlideNumber: 'all',
@@ -715,7 +719,7 @@ <h2>Deliverables</h2>
         },
 
         // reveal.js plugins
-        plugins: [QuartoLineHighlight, PdfExport, RevealMenu, QuartoSupport,
+        plugins: [QuartoLineHighlight, PdfExport, RevealMenu, RevealChalkboard, QuartoSupport,
 
           RevealMath,
           RevealNotes,
diff --git a/_site/search.json b/_site/search.json
index fcbd167..0ea1744 100644
--- a/_site/search.json
+++ b/_site/search.json
@@ -431,6 +431,6 @@
     "href": "omics/week-3/study_before_workshop.html#deliverables",
     "title": "Independent Study to prepare for workshop",
     "section": "Deliverables",
-    "text": "Deliverables\n\nDescribe the data\n\nNumber of cells/samples/reps/treatments\nnumber of genes\ntype of expression values\nprior processing\nmissing values\noverview of expression\nclustering of genes/samples\n\nReport on differential expression between two groups\n\nnumber of DE at 1%, 5% and 10%.\ntable of expression, fold changes, signifcance at each sig.\nVolcano plot\n\nReport list of marker candidate gene IDs for a cell type of choice. Justify filters. Table with fold FC, p values, IDs, canonical gene names\nInterpret the biology by reporting on a few group of genes and the processes in which they are involved.\nReport on your chosen genes and explain why you think they are good candidates for follow up work\n\n\n\n\n\n\n\nNestorowa, Sonia, Fiona K. Hamey, Blanca Pijuan Sala, Evangelia Diamanti, Mairi Shepherd, Elisa Laurenti, Nicola K. Wilson, David G. Kent, and Berthold Göttgens. 2016. “A Single-Cell Resolution Map of Mouse Hematopoietic Stem and Progenitor Cell Differentiation.” Blood 128 (8): e20–31. https://doi.org/10.1182/blood-2016-05-716480."
+    "text": "Deliverables\n\nDescribe the data\n\nNumber of cells/samples/reps/treatments\nnumber of genes\ntype of expression values\nprior processing\nmissing values\noverview of expression\nclustering of genes/samples\n\nReport on differential expression between two groups\n\nnumber of DE at 1%, 5% and 10%.\ntable of expression, fold changes, signifcance at each sig.\nVolcano plot\n\nReport list of marker candidate gene IDs for a cell type of choice. Justify filters. Table with fold FC, p values, IDs, canonical gene names\nInterpret the biology by reporting on a few group of genes and the processes in which they are involved.\nReport on your chosen genes and explain why you think they are good candidates for follow up work\n\n\n\n🔗 About Omics 1: Hello data!\n\n\n\nNestorowa, Sonia, Fiona K. Hamey, Blanca Pijuan Sala, Evangelia Diamanti, Mairi Shepherd, Elisa Laurenti, Nicola K. Wilson, David G. Kent, and Berthold Göttgens. 2016. “A Single-Cell Resolution Map of Mouse Hematopoietic Stem and Progenitor Cell Differentiation.” Blood 128 (8): e20–31. https://doi.org/10.1182/blood-2016-05-716480."
   }
 ]
\ No newline at end of file
diff --git a/_site/site_libs/revealjs/plugin/reveal-chalkboard/README.md b/_site/site_libs/revealjs/plugin/reveal-chalkboard/README.md
new file mode 100644
index 0000000..7391a00
--- /dev/null
+++ b/_site/site_libs/revealjs/plugin/reveal-chalkboard/README.md
@@ -0,0 +1,160 @@
+# Chalkboard
+
+With this plugin you can add a chalkboard to reveal.js. The plugin provides two possibilities to include handwritten notes to your presentation:
+
+- you can make notes directly on the slides, e.g. to comment on certain aspects,
+- you can open a chalkboard or whiteboard on which you can make notes.
+
+The main use case in mind when implementing the plugin is classroom usage in which you may want to explain some course content and quickly need to make some notes.
+
+The plugin records all drawings made so that they can be play backed using the `autoSlide` feature or the `audio-slideshow` plugin.
+
+[Check out the live demo](https://rajgoel.github.io/reveal.js-demos/chalkboard-demo.html)
+
+The chalkboard effect is based on [Chalkboard](https://github.com/mmoustafa/Chalkboard) by Mohamed Moustafa.
+
+## Installation
+
+Copy the file `plugin.js` and the  `img` directory into the plugin folder of your reveal.js presentation, i.e. `plugin/chalkboard` and load the plugin as shown below.
+
+```html
+<script src="plugin/chalkboard/plugin.js"></script>
+<script src="plugin/customcontrols/plugin.js"></script>
+
+<script>
+    Reveal.initialize({
+        // ...
+        plugins: [ RevealChalkboard, RevealCustomControls ],
+        // ...
+    });
+</script>
+```
+
+The following stylesheet
+```html
+<link rel="stylesheet" href="plugin/chalkboard/style.css">
+<link rel="stylesheet" href="plugin/customcontrols/style.css">
+```
+has to be included to the `head` section of you HTML-file.
+
+
+In order to include buttons for opening and closing the notes canvas or the chalkboard you should make sure that `font-awesome` is available. The easiest way is to include
+```
+<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/font-awesome/4.5.0/css/font-awesome.min.css">
+```
+to the ```head``` section of you HTML-file.
+
+## Usage
+
+### Mouse or touch
+- Click on the pen symbols at the bottom left to toggle the notes canvas or chalkboard
+- Click on the color picker at the left to change the color (the color picker is only visible if the notes canvas or chalkboard is active)
+- Click on the up/down arrows on the left to the switch among multiple chalkboardd (the up/down arrows are only available for the chlakboard)
+- Click the left mouse button and drag to write on notes canvas or chalkboard
+- Click the right mouse button and drag to wipe away previous drawings
+- Touch and move to write on notes canvas or chalkboard
+- Touch and hold for half a second, then move to wipe away previous drawings
+
+### Keyboard
+- Press the 'BACKSPACE' key to delete all chalkboard drawings
+- Press the 'DEL' key to clear the notes canvas or chalkboard
+- Press the 'c' key to toggle the notes canvas
+- Press the 'b' key to toggle the chalkboard
+- Press the 'd' key to download drawings
+- Press the 'x' key to cycle colors forward
+- Press the 'y' key to cycle colors backward
+
+## Playback
+
+If the `autoSlide` feature is set or if the `audio-slideshow` plugin is used, pre-recorded chalkboard drawings can be played. The slideshow plays back the user interaction with the chalkboard in the same way as it was conducted when recording the data.
+
+## Multiplexing
+
+The plugin supports multiplexing via the [`multiplex` plugin](https://github.com/reveal/multiplex) or the [`seminar` plugin](https://github.com/rajgoel/reveal.js-plugins/tree/master/seminar).
+
+## PDF-Export
+
+If the slideshow is opened in [print mode](https://revealjs.com/pdf-export/), the chalkboard drawings in the session storage (see `storage` option - print version must be opened in the same tab or window as the original slideshow) or provided in a file (see `src` option) are included in the PDF-file. Each drawing on the chalkboard is added after the slide that was shown when opening the chalkboard. Drawings on the notes canvas are not included in the PDF-file.
+
+
+## Configuration
+
+The plugin has several configuration options:
+
+- ```boardmarkerWidth```: an integer, the drawing width of the boardmarker; larger values draw thicker lines.
+- ```chalkWidth```: an integer, the drawing width of the chalk; larger values draw thicker lines.
+- ```chalkEffect```: a float in the range ```[0.0, 1.0]```, the intesity of the chalk effect on the chalk board. Full effect (default) ```1.0```, no effect ```0.0```.
+- ```storage```: Optional variable name for session storage of drawings.
+- ```src```: Optional filename for pre-recorded drawings.
+- ```readOnly```: Configuation option allowing to prevent changes to existing drawings. If set to ```true``` no changes can be made, if set to false ```false``` changes can be made, if unset or set to ```undefined``` no changes to the drawings can be made after returning to a slide or fragment for which drawings had been recorded before. In any case the recorded drawings for a slide or fragment can be cleared by pressing the 'DEL' key (i.e. by using the ```RevealChalkboard.clear()``` function).
+- ```transition```: Gives the duration (in milliseconds) of the transition for a slide change, so that the notes canvas is drawn after the transition is completed.
+- ```theme```: Can be set to either ```"chalkboard"``` or ```"whiteboard"```.
+
+The following configuration options allow to change the appearance of the notes canvas and the chalkboard. All of these options require two values, the first gives the value for the notes canvas, the second for the chalkboard.
+
+- ```background```: The first value expects a (semi-)transparent color which is used to provide visual feedback that the notes canvas is enabled, the second value expects a filename to a background image for the chalkboard.
+- ```grid```: By default whiteboard and chalkboard themes include a grid pattern on the background. This pattern can be modified by setting the color, the distance between lines, and the line width, e.g. ```{ color: 'rgb(127,127,255,0.1)', distance: 40, width: 2}```. Alternatively, the grid can be removed by setting the value to ```false```.
+- ```eraser```: An image path and radius for the eraser.
+- ```boardmarkers```: A list of boardmarkers with given color and cursor.
+- ```chalks```: A list of chalks with given color and cursor.
+- ```rememberColor```: Whether to remember the last selected color for the slide canvas or the board.
+
+All of the configurations are optional and the default values shown below are used if the options are not provided.
+
+```javascript
+Reveal.initialize({
+	// ...
+    chalkboard: {
+        boardmarkerWidth: 3,
+        chalkWidth: 7,
+        chalkEffect: 1.0,
+        storage: null,
+        src: null,
+        readOnly: undefined,
+        transition: 800,
+        theme: "chalkboard",
+        background: [ 'rgba(127,127,127,.1)' , path + 'img/blackboard.png' ],
+        grid: { color: 'rgb(50,50,10,0.5)', distance: 80, width: 2},
+        eraser: { src: path + 'img/sponge.png', radius: 20},
+        boardmarkers : [
+                { color: 'rgba(100,100,100,1)', cursor: 'url(' + path + 'img/boardmarker-black.png), auto'},
+                { color: 'rgba(30,144,255, 1)', cursor: 'url(' + path + 'img/boardmarker-blue.png), auto'},
+                { color: 'rgba(220,20,60,1)', cursor: 'url(' + path + 'img/boardmarker-red.png), auto'},
+                { color: 'rgba(50,205,50,1)', cursor: 'url(' + path + 'img/boardmarker-green.png), auto'},
+                { color: 'rgba(255,140,0,1)', cursor: 'url(' + path + 'img/boardmarker-orange.png), auto'},
+                { color: 'rgba(150,0,20150,1)', cursor: 'url(' + path + 'img/boardmarker-purple.png), auto'},
+                { color: 'rgba(255,220,0,1)', cursor: 'url(' + path + 'img/boardmarker-yellow.png), auto'}
+        ],
+        chalks: [
+                { color: 'rgba(255,255,255,0.5)', cursor: 'url(' + path + 'img/chalk-white.png), auto'},
+                { color: 'rgba(96, 154, 244, 0.5)', cursor: 'url(' + path + 'img/chalk-blue.png), auto'},
+                { color: 'rgba(237, 20, 28, 0.5)', cursor: 'url(' + path + 'img/chalk-red.png), auto'},
+                { color: 'rgba(20, 237, 28, 0.5)', cursor: 'url(' + path + 'img/chalk-green.png), auto'},
+                { color: 'rgba(220, 133, 41, 0.5)', cursor: 'url(' + path + 'img/chalk-orange.png), auto'},
+                { color: 'rgba(220,0,220,0.5)', cursor: 'url(' + path + 'img/chalk-purple.png), auto'},
+                { color: 'rgba(255,220,0,0.5)', cursor: 'url(' + path + 'img/chalk-yellow.png), auto'}
+        ]
+    },
+    customcontrols: {
+  		controls: [
+  			{ icon: '<i class="fa fa-pen-square"></i>',
+  			  title: 'Toggle chalkboard (B)',
+  			  action: 'RevealChalkboard.toggleChalkboard();'
+  			},
+  			{ icon: '<i class="fa fa-pen"></i>',
+  			  title: 'Toggle notes canvas (C)',
+  			  action: 'RevealChalkboard.toggleNotesCanvas();'
+  			}
+  		]
+    },
+    // ...
+
+});
+```
+
+
+## License
+
+MIT licensed
+
+Copyright (C) 2021 Asvin Goel
diff --git a/_site/site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/webfonts/fa-brands-400.woff2 b/_site/site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/webfonts/fa-brands-400.woff2
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diff --git a/_site/site_libs/revealjs/plugin/reveal-chalkboard/img/sponge.png b/_site/site_libs/revealjs/plugin/reveal-chalkboard/img/sponge.png
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diff --git a/_site/site_libs/revealjs/plugin/reveal-chalkboard/img/whiteboard.png b/_site/site_libs/revealjs/plugin/reveal-chalkboard/img/whiteboard.png
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diff --git a/core/core.qmd b/core/core.qmd
index ad995fa..f2c5334 100644
--- a/core/core.qmd
+++ b/core/core.qmd
@@ -11,24 +11,18 @@ Good organisation is important because you will want to be able to set work asid
 
 ## Week 1 Core 1 Organising reproducible data analyses
 
-This week you will revise some essential concepts for scientific computing: file system organisation, file types, working directories and paths. The workshop will cover a rationale for working reproducibly, project oriented workflow, naming things and documenting your work. We will also examine some file types and the concept of tidy data.
+This week you will revise some essential concepts for scientific computing: file system organisation, file types, working directories and paths. The workshop will cover a rationale for working reproducibly, project oriented workflow, naming things and documenting your work.
 
 
-## Week 2 Core 2 Workflow tips
+## Week 2 Core 2 File types, workflow tips and other tools
 
 <!-- Before  -->
 <!-- Apply to GitHub Global Campus as a student -->
 
-<!-- -   Reference managers: Zotero -->
-<!-- -   github copilot -->
-<!-- -   chat gtp -->
-<!-- -   Data management -->
-<!--     -   google drive: https://www.york.ac.uk/it-services/services/drive/#tab-6 -->
 
 
-<!-- Workshop -->
 
-<!-- Code formatting and style, 😎 Cool code Tips, Code 'algorithmically.', Writing functions (R and python??) (BIO00058M-Data-science-2020/slides/03_repro_and_intro_to_rmarkdown) -->
+
 
 
 <!-- After -->
diff --git a/core/week-1/styles.css b/core/week-1/styles.css
new file mode 100644
index 0000000..2ff0570
--- /dev/null
+++ b/core/week-1/styles.css
@@ -0,0 +1,16 @@
+/* css styles */
+
+
+@import url('https://fonts.googleapis.com/css2?family=Open+Sans&family=Source+Code+Pro&display=swap');
+
+
+// fonts
+
+$font-family-monospace: "Source Code Pro";
+
+/*-- scss:rules --*/
+
+code.sourceCode {
+  font-size: 1.3em;
+}
+
diff --git a/core/week-2/chalkboard.json b/core/week-2/chalkboard.json
new file mode 100644
index 0000000..9d5c016
--- /dev/null
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--- a/core/week-2/overview.qmd
+++ b/core/week-2/overview.qmd
@@ -1,33 +1,42 @@
 ---
 title: "Overview"
-subtitle: "Core 2:  Workflow tips"
+subtitle: "Core 2: File types, workflow tips and other tools"
 ---
 
-xxxxx
+This week
 
 ### Learning objectives
 
--   dd
--   dd.
--   dd
--   d
+The successful student will be able to:
+
+-   explain why RStudio are useful/essential and be able to use the **`usethis`** package 
+-   write cool 😎 code not 😩 ugly code
+-   explain the value of code which expresses the structure of the problem/solution.
+-   describe some common file types for biological data
+-   use some useful shortcuts to help write cool 😎 code
+-   know what the command line is and how to use it for simple tasks
+-   use Google colab to run code
+-   recognise some of the differences between R and Python
 
 ### Instructions
 
-1.  [Prepare](study_before_workshop.qmd)
+1.  [Prepare](study_before_workshop.qmd) 20 mins reading on RStudio Projects revisited, formatting code and coding algorithmically
 
-    i.  📖 Read 
 
 2.  [Workshop](workshop.qmd)
 
-    i.  💻 dd.
+    i.  💬 Types of biological data files
 
-    ii. 💻 ddd
+    ii. 🪄 Workflow tips and shortcuts
 
-    iii. 💻 ddd
+    iii. 💻 The command line
+    
+    iv.  💻 Google colab
+    
+    v.  💻 Python
 
 3.  [Consolidate](study_after_workshop.qmd)
 
-    i.  💻 dd
+    i.  💻 not sure yet :)
+
 
-    ii. 💻 dd
diff --git a/core/week-2/study_after_workshop.qmd b/core/week-2/study_after_workshop.qmd
index f47370e..6b4c2fa 100644
--- a/core/week-2/study_after_workshop.qmd
+++ b/core/week-2/study_after_workshop.qmd
@@ -7,19 +7,4 @@ format:
     code-summary: "Answer - don't look until you have tried!"
 ---
 
-# Set up
-
-If you have just opened RStudio you will want to load the packages and import the data.
-
-```{r}
-#| code-fold: false
-library(tidyverse)
-library(readxl)
-```
-
-1.  💻 xx.
-
-```{r}
-
- 
-```
+# bbbb
\ No newline at end of file
diff --git a/core/week-2/study_before_workshop.ipynb b/core/week-2/study_before_workshop.ipynb
new file mode 100644
index 0000000..c86b52c
--- /dev/null
+++ b/core/week-2/study_before_workshop.ipynb
@@ -0,0 +1,156 @@
+{
+  "cells": [
+    {
+      "cell_type": "raw",
+      "metadata": {},
+      "source": [
+        "---\n",
+        "title: \"Independent Study to prepare for workshop\"\n",
+        "subtitle: \"Core 2: File types, workflow tips and other tools\"\n",
+        "author: \"Emma Rand\"\n",
+        "format: \n",
+        "  revealjs:\n",
+        "    footer: \"🔗 [About Core 2: File types, workflow tips and other tools](https://3mmarand.github.io/BIO00088H-data/core/week-2/overview.html)\"\n",
+        "    slide-number: true\n",
+        "    chalkboard: true\n",
+        "    code-link: true\n",
+        "    code-line-numbers: false\n",
+        "bibliography: ../../references.bib\n",
+        "editor: \n",
+        "  markdown: \n",
+        "    wrap: 72\n",
+        "---"
+      ],
+      "id": "05ff7dda"
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "## Overview\n",
+        "\n",
+        "-   RStudio Projects revisited\n",
+        "\n",
+        "## RStudio Projects\n",
+        "\n",
+        "::: incremental\n",
+        "-   We used RStudio Projects in stage one but they are so useful, it is\n",
+        "    worth covering them in case you are not yet using them.\n",
+        "\n",
+        "-   RStudio Projects make it easy to manage working directories and\n",
+        "    paths because they set the working directory to the RStudio Projects\n",
+        "    directory automatically.\n",
+        ":::\n",
+        "\n",
+        "# Option 1: `code-line-numbers`\n",
+        "\n",
+        "## RStudio Projects\n",
+        "\n",
+        "::: columns\n",
+        "::: {.column width=\"70%\"}\n",
+        "\n",
+        "```{bash}\n",
+        "#| eval: false\n",
+        "#| code-line-numbers: \"1\"\n",
+        "-- stem_cell_rna\n",
+        "   |__stem_cell_rna.Rproj   \n",
+        "   |__raw_ data/            \n",
+        "      |__2019-03-21_donor_1.csv\n",
+        "   |__README. md\n",
+        "   |__LICENSE\n",
+        "   |__R/\n",
+        "      |__01_data_processing.R\n",
+        "      |__02_exploratory.R\n",
+        "      |__functions/\n",
+        "         |__101 file import\n",
+        "         |__02_normalise.R\n",
+        "```\n",
+        "\n",
+        ":::\n",
+        "\n",
+        "::: {.column width=\"30%\"}\n",
+        "The project directory\n",
+        ":::\n",
+        ":::\n",
+        "\n",
+        "## RStudio Projects\n",
+        "\n",
+        "::: columns\n",
+        "::: {.column width=\"70%\"}\n",
+        "\n",
+        "```{bash}\n",
+        "#| eval: false\n",
+        "#| code-line-numbers: \"2\"\n",
+        "-- stem_cell_rna\n",
+        "   |__stem_cell_rna.Rproj   \n",
+        "   |__raw_ data/            \n",
+        "      |__2019-03-21_donor_1.csv\n",
+        "   |__README. md\n",
+        "   |__LICENSE\n",
+        "   |__R/\n",
+        "      |__01_data_processing.R\n",
+        "      |__02_exploratory.R\n",
+        "      |__functions/\n",
+        "         |__101 file import\n",
+        "         |__02_normalise.R\n",
+        "```\n",
+        "\n",
+        ":::\n",
+        "\n",
+        "::: {.column width=\"30%\"}\n",
+        "the .RProj file which is the defining feature of an Studio Project\n",
+        ":::\n",
+        ":::\n",
+        "\n",
+        "## RStudio Projects\n",
+        "\n",
+        "::: incremental\n",
+        "-   When you open an RStudio Project, the working directory is set to\n",
+        "    the Project directory (i.e., the location of the `.Rproj` file).\n",
+        "\n",
+        "-   When you use an RStudio Project you do not need to use `setwd()`\n",
+        ":::\n",
+        "\n",
+        "## RStudio Projects\n",
+        "\n",
+        "![Jenny Bryan](images/JennyBryan.jpg){width=\"300\"}\n",
+        "\n",
+        "In the words of [Jenny\n",
+        "Bryan](https://www.tidyverse.org/blog/2017/12/workflow-vs-script/):\n",
+        "\n",
+        "> if the first line of your R script is\n",
+        "> setwd(\"C:\\Users\\jenny\\path\\that\\only\\I\\have\") I will come into your\n",
+        "> office and SET YOUR COMPUTER ON FIRE.\n",
+        "\n",
+        ". . .\n",
+        "\n",
+        "Creating a 'project' in RStudio sets your working directory in a way\n",
+        "that's portable across machines.\n",
+        "\n",
+        "## \n",
+        "\n",
+        "## \n",
+        "\n",
+        "## \n",
+        "\n",
+        "## Code formatting and style,\n",
+        "\n",
+        "😎 Cool code Tips, Code 'algorithmically.',\n",
+        "\n",
+        "Writing functions (R and python??)\n",
+        "\n",
+        "install.packages(\"styler\")"
+      ],
+      "id": "01af4bb6"
+    }
+  ],
+  "metadata": {
+    "kernelspec": {
+      "display_name": "Python 3",
+      "language": "python",
+      "name": "python3"
+    }
+  },
+  "nbformat": 4,
+  "nbformat_minor": 5
+}
\ No newline at end of file
diff --git a/core/week-2/study_before_workshop.qmd b/core/week-2/study_before_workshop.qmd
index 95b15d6..01e70dc 100644
--- a/core/week-2/study_before_workshop.qmd
+++ b/core/week-2/study_before_workshop.qmd
@@ -1,6 +1,536 @@
 ---
 title: "Independent Study to prepare for workshop"
-subtitle: "Core 2"
+subtitle: "Core 2: File types, workflow tips and other tools"
+author: "Emma Rand"
+format: 
+  revealjs:
+    css: styles.css
+    footer: "🔗 [About Core 2: File types, workflow tips and other tools](https://3mmarand.github.io/BIO00088H-data/core/week-2/overview.html)"
+    slide-number: true
+    chalkboard: true
+    code-link: true
+    code-line-numbers: false
+bibliography: ../../references.bib
+editor: 
+  markdown: 
+    wrap: 72
+engine: knitr
 ---
 
-1.  📖 Read xxxx
+
+## Overview
+
+
+-   RStudio Projects revisited
+    -   using **`usethis`** package
+    -   Adding a README
+-   Formatting code
+-   Code algorithmically / algebraically.
+
+
+## Reproducibility is a continuum
+
+Some is better than none!
+
+-   Organise your project   
+-   Script **everything**.  
+-   Format code and follow a consistent style.  
+-   Code algorithmically 
+-   Modularise your code: organise into sections and scripts 
+-   Document your project - commenting, READMEs 
+-   Use literate programming e.g., R Markdown or Quarto
+
+. . .
+
+-   More advanced: Version control, continuous integration, environments, containers
+
+# RStudio Projects revisited
+
+## RStudio Projects
+
+::: incremental
+
+-   We used RStudio Projects in stage one but they are so useful, it is
+    worth covering them again in case you are not yet using them.
+    
+-   We will also cover the **`usethis`**workflow to create an RStudio
+    Project.
+
+-   RStudio Projects make it easy to manage working directories and
+    paths because they set the working directory to the RStudio Projects
+    directory automatically.
+:::
+
+## RStudio Projects
+
+::: columns
+::: {.column width="60%"}
+```{bash}
+#| eval: false
+#| code-line-numbers: "1"
+-- stem_cell_rna
+   |__stem_cell_rna.Rproj   
+   |__raw_ data/            
+      |__2019-03-21_donor_1.csv
+   |__README. md
+   |__R/
+      |__01_data_processing.R
+      |__02_exploratory.R
+      |__functions/
+         |__theme_volcano.R
+         |__normalise.R
+```
+:::
+
+::: {.column width="40%"}
+The project directory is the folder at the top [^1]
+:::
+:::
+
+[^1]: Thanks to [Mine
+    Çetinkaya-Rundel](https://mastodon.social/@minecr@fosstodon.org) who
+    helped me work out how to highlight a line
+    <https://gist.github.com/mine-cetinkaya-rundel/3af3415eab70a65be3791c3dcff6e2e3>.
+    Note to futureself: the `engine: knitr` matters.
+
+## RStudio Projects
+
+::: columns
+::: {.column width="60%"}
+```{bash}
+#| eval: false
+#| code-line-numbers: "2"
+-- stem_cell_rna
+   |__stem_cell_rna.Rproj   
+   |__raw_ data/            
+      |__2019-03-21_donor_1.csv
+   |__README. md
+   |__R/
+      |__01_data_processing.R
+      |__02_exploratory.R
+      |__functions/
+         |__theme_volcano.R
+         |__normalise.R
+```
+:::
+
+::: {.column width="40%"}
+the `.RProj` file is directly under the project folder. Its presence is what makes the folder an RStudio Project
+:::
+:::
+
+## RStudio Projects
+
+::: incremental
+-   When you open an RStudio Project, the working directory is set to
+    the Project directory (i.e., the location of the `.Rproj` file).
+
+-   When you use an RStudio Project you do not need to use `setwd()`
+
+-   When someone, including future you, opens the project on another
+    machine, all the paths just work.
+:::
+
+## RStudio Projects
+
+![Jenny Bryan](images/JennyBryan.jpg){fig-align="left" width="400"}
+
+In the words of [Jenny
+Bryan](https://www.tidyverse.org/blog/2017/12/workflow-vs-script/):
+
+> "If the first line of your R script is
+> setwd("C:/Users/jenny/path/that/only/I/have") I will come into your
+> office and SET YOUR COMPUTER ON FIRE"
+
+## Creating an RStudio Project
+
+There are two ways to create an RStudio Project.
+
+1.  Using one of the two menus
+
+2.  Using the **`usethis`** package
+
+## Using a menu
+
+There are two menus:
+
+1.  Top left, File menu
+
+2.  Top Right, drop-down indicated by the `.RProj` icon
+
+They both do the same thing. 
+
+In both cases you choose: New Project \| New Directory \| New Project
+
+. . .
+
+Make sure you "Browse" to the folder you want to create the project.
+
+
+# Using the **`usethis`** package
+
+
+## Using the **`usethis`** package
+
+I occasionally use the menu but I mostly use the **`usethis`** package.
+
+. . .
+
+🎬 Go to RStudio and check your working directory:
+
+```{r}
+#| eval: false
+getwd()
+```
+
+`"C:/Users/er13/Desktop"`
+
+. . .
+
+❔ Is your working directory a good place to create a Project folder?
+
+## Using the **`usethis`** package
+
+If this is a good place to create a Project directory then...
+
+🎬 Create a project with:
+
+```{r}
+#| eval: false
+usethis::create_project("bananas")
+```
+
+## Using the **`usethis`** package
+
+Otherwise
+
+If you want the project directory elsewhere, you will need to give the
+relative path, e.g.
+
+```{r}
+#| eval: false
+usethis::create_project("../Documents/bananas")
+```
+
+## Using the **`usethis`** package
+
+The output will look like this and a new RStudio session will start.
+
+```         
+> usethis::create_project("bananas")
+√ Creating 'bananas/'
+√ Setting active project to 'C:/Users/er13/Desktop/bananas'
+√ Creating 'R/'
+√ Writing 'bananas.Rproj'
+√ Adding '.Rproj.user' to '.gitignore'
+√ Opening 'C:/Users/er13/Desktop/bananas/' in new RStudio session
+√ Setting active project to '<no active project>'
+```
+
+## Using the **`usethis`** package
+
+When you create a new RStudio Project with **`usethis`**:
+
+::: incremental
+
+-   A folder called `bananas/` is created
+-   RStudio starts a new session in `bananas/` i.e., your working
+    directory is now `bananas/`
+-   A folder called `R/` is created
+-   A file called `bananas.Rproj` is created
+-   A file called `.gitignore` is created
+-   A hidden directory called `.Rproj.user` is created
+
+:::
+
+## Using the **`usethis`** package
+
+::: incremental
+-   the `.Rproj` file is what makes the directory an RStudio Project
+
+-   the `Rproj.user` directory is where project-specific temporary files
+    are stored. You don't need to mess with it.
+
+-   the `.gitignore` is used for version controlled projects. If not using git, 
+    you can ignore it.
+:::
+
+## Opening and closing
+
+You can close an RStudio Project with ONE of:
+
+1.  File \| Close Project
+2.  Using the drop-down option on the far right of the tool bar where
+    you see the Project name
+
+. . .
+
+You can open an RStudio Project with ONE of:
+
+1.  File \| Open Project or File \| Recent Projects\
+2.  Using the drop-down option on the far right of the tool bar where
+    you see the Project name\
+3.  Double-clicking an .Rproj file from your file explorer/finder
+
+When you open project, a new R session starts.
+
+# Adding a README
+
+## Using the **`usethis`** package
+
+Once the RStudio project has been created, **`usethis`** helps you
+follow good practice.
+
+. . .
+
+🎬 We can add a README with:
+
+```{r}
+#| eval: false
+usethis::use_readme_md()
+```
+
+. . . 
+
+This creates a file called `README.md`, with a little default text, in
+the Project directory and opens it for editing.
+
+. . .
+
+`md` stands for markdown, it is a extremely widely used text formatting language which is readable as plain text. If you have ever used asterisks to make text bold or italic, you have used markdown.
+
+
+#  Code formatting and style
+
+
+##  Code formatting and style
+
+> "Good coding style is like correct punctuation: you can manage without it, butitsuremakesthingseasiertoread."
+
+[The tidyverse style guide](https://style.tidyverse.org/) 
+
+##  Code formatting and style
+
+We have all written code which is hard to read! 
+
+We all improve over time.
+
+```{r}
+#| echo: false
+tweetrmd::include_tweet("https://twitter.com/hadleywickham/status/589068687669243905")
+```
+
+
+
+##  Code formatting and style
+
+Some keys points:
+
+-   be consistent, emulate experienced coders  
+-   use snake_case for variable names (not CamelCase, dot.case)  
+-   use `<-` not `=` for assignment  
+-   use spacing around most operators and after commas  
+-   use indentation  
+-   avoid long lines, break up code blocks with new lines  
+-   use `"` for quoting text (not `'`) unless the text contains double quotes  
+
+
+
+## 😩 Ugly code 😩
+
+
+
+```{r}
+#| eval: false
+data<-read_csv('../data-raw/Y101_Y102_Y201_Y202_Y101-5.csv',skip=2)
+library(janitor);sol<-clean_names(data)
+data=data|>filter(str_detect(description,"OS=Homo sapiens"))|>filter(x1pep=='x')
+data=data|>
+mutate(g=str_extract(description,
+"GN=[^\\s]+")|>str_replace("GN=",''))
+data<-data|>mutate(id=str_extract(accession,"1::[^;]+")|>str_replace("1::",""))
+```
+
+
+## 😩 Ugly code 😩
+
+-   no spacing or indentation
+-   inconsistent splitting of code blocks over lines
+-   inconsistent use of quote characters
+-   no comments
+-   variable names convey no meaning
+-   use of `=` for assignment and inconsistently
+-   multiple commands on a line
+-   library statement in the middle of the analysis
+
+
+
+## 😎 Cool code 😎
+
+
+```{r}
+#| eval: false
+
+# Packages ----------------------------------------------------------------
+library(tidyverse)
+library(janitor)
+
+# Import ------------------------------------------------------------------
+
+# define file name
+file <- "../data-raw/Y101_Y102_Y201_Y202_Y101-5.csv"
+
+# import: column headers and data are from row 3
+solu_protein <- read_csv(file, skip = 2) |>
+  janitor::clean_names()
+
+# Tidy data ----------------------------------------------------------------
+
+# filter out the bovine proteins and those proteins 
+# identified from fewer than 2 peptides
+solu_protein <- solu_protein |>
+  filter(str_detect(description, "OS=Homo sapiens")) |>
+  filter(x1pep == "x")
+
+# Extract the genename from description column to a column
+# of its own
+solu_protein <- solu_protein |>
+  mutate(genename =  str_extract(description,"GN=[^\\s]+") |>
+           str_replace("GN=", ""))
+
+# Extract the top protein identifier from accession column (first
+# Uniprot ID after "1::") to a column of its own
+solu_protein <- solu_protein |>
+  mutate(protid =  str_extract(accession, "1::[^;]+") |>
+           str_replace("1::", ""))
+```
+
+
+## 😎 Cool code 😎
+
+-   `library()` calls collected
+
+-   Uses code sections to make it easier to navigate
+
+-   Uses white space and proper indentation
+
+-   Commented
+
+-   Uses more informative name for the dataframe
+
+
+
+# Code 'algorithmically'
+
+
+##  Code 'algorithmically'
+
+::: incremental
+
+-   Write code which expresses the structure of the problem/solution.
+
+-   Avoid hard coding numbers if at all possible - declare variables instead
+
+-   Declare frequently used values as variables at the start e.g., colour schemes, figure saving settings
+
+:::
+
+## 😩 Hard coding numbers.
+
+::: incremental
+
+-   Suppose we want to calculate the sums of squares, $SS(x)$, for the number of eggs in five nests. 
+
+-   The formula is given by: $\sum (x_i- \bar{x})^2$  
+
+-   We could calculate the mean and copy it, and the individual numbers into the formula
+
+:::
+
+## 😩 Hard coding numbers.
+
+```{r}
+# mean number of eggs per nest
+sum(3, 5, 6, 7, 8) / 5
+
+# ss(x) of number of eggs
+(3 - 5.8)^2 + (5 - 5.8)^2 + (6 - 5.8)^2 + (7 - 5.8)^2 + (8 - 5.8)^2
+```
+
+
+I am coding the calculation of the mean rather using the `mean()` function only to explain what 'coding algorithmically' means using a simple example.
+
+
+## 😩 Hard coding numbers
+
+::: incremental
+
+-   if any of the sample numbers must be altered, all the code needs changing
+
+-   it is hard to tell that the output of the first line is a mean
+
+-   its hard to recognise that the numbers in the mean calculation correspond to those in the next calculation
+
+-   it is hard to tell that 5 is just the number of nests
+
+-   no way of know if numbers are the same by coincidence or they refer to the same thing
+
+:::
+
+## 😎 Better
+
+```{r}
+# eggs each nest
+eggs <- c(3, 5, 6, 7, 8)
+
+# mean eggs per nest
+mean_eggs <- sum(eggs) / length(eggs)
+
+# ss(x) of number of eggs
+sum((eggs - mean_eggs)^2)
+```
+
+## 😎 Better
+
+::: incremental
+
+-   the commenting is similar but it is easier to follow
+
+-   if any of the sample numbers must be altered, only that number needs changing
+
+-   assigning a value you will later use to a variable with a meaningful name allows us to understand the first and second calculations
+
+-   makes use of R's elementwise calculation which resembles the formula (i.e., is expressed as the general rule)
+
+:::
+
+## Summary
+
+::: incremental
+
+-  Use an RStudio project for any R work (you can also incorporate other languages)
+
+-  Write Cool code not Ugly code: space, consistency, indentation, comments, meaningful variable names
+
+-  Write code which expresses the structure of the problem/solution.
+
+-  Avoid hard coding numbers if at all possible - declare variables instead
+
+:::
+
+# Reading
+
+Recommended if you still need convincing to use RStudio Projects
+
+-   [Project-oriented workflow \| What They Forgot to Teach You About
+    R](https://rstats.wtf/projects) [@bryan]
+
+Completely optional suggestions for further reading
+
+-   Ten simple rules for reproducible computational research
+    [@sandve2013]
+-   Good enough practices in scientific computing [@wilson2017]
+-   Excuse Me, Do You Have a Moment to Talk About Version Control?
+    [@bryan2018]
+
+## References
\ No newline at end of file
diff --git a/core/week-2/workshop.qmd b/core/week-2/workshop.qmd
index 391994c..91a3dcc 100644
--- a/core/week-2/workshop.qmd
+++ b/core/week-2/workshop.qmd
@@ -1,6 +1,6 @@
 ---
 title: "Workshop"
-subtitle: "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx"
+subtitle: "File types, workflow tips and other tools"
 author: "Emma Rand"
 toc: true
 toc-depth: 4
@@ -13,63 +13,120 @@ bibliography: ../../references.bib
 editor: 
   markdown: 
     wrap: 72
+engine: knitr
 ---
 
-```{r}
-#| include: false
-library(tidyverse)
-```
-
 # Introduction
 
-
 ## Session overview
 
-In this workshop you will 
+In this workshop you will
+
+
 
+# File formats
 
-## File formats
 
-Data files. 
+Types of Data files. 
 -   Sequences data 
 -   Image data 
 -  Structure data PDB/mmCIF  www.pdb.org
 
 Similarities and differences
 
-🎬 
+## Getting started
 
-what is markdown
+Make a new RStudio project (use the workflow from in the independent
+study
 
+Tips
 
-Google Colab
+multiple cursors
 
-snippets
+open a file
 
-python
+the command pallette, 
 
-differences between r and python
+segmenting code
 
-rstudio terminal
+to correct indentation CONTROL+i
 
-basic bash
+to reformat code CONTROL+SHIFT+A Not perfect but corrects spacing, indentation, multiple commands on lines and assignment with `=`
 
-You're finished!
 
-# 🥳 Well Done! 🎉
+to comment and uncomment lines CONTROL+SHIFT+C
+
+show the margin Tools | Global Options | Code
+
 
 
 
+restart R
+
+# The command line
+
+The command line - or shell - is a text interface for your computer.
+It's a program that takes in commands, which it passes on to the
+computer's operating system to run.
+
+## RStudio terminal
+
+The RStudio terminal is a convenient interface to the shell without
+leaving RStudio. It is useful for running commands that are not
+available in R. For example, you can use it to run other programs like
+fasqc, git, ftp, ssh
+
+```{bash}
+pwd
+```
+
+```{bash}
+ls
+```
+
+```{bash}
+ls -l
+```
+
+```{bash}
+ls -F
+```
+
+# Google Colab
+
+# Python
+
+## Differences between R and python
+
+
+## Quarto note books
+
+zotero
+
+🎬
+
+You're finished!
+
+# 🥳 Well Done! 🎉
+
 # Independent study following the workshop
 
 [Consolidate](study_after_workshop.qmd)
 
 # The Code file
 
-These contain all the code needed in the workshop even where it is not visible on the webpage.
+These contain all the code needed in the workshop even where it is not
+visible on the webpage.
 
-The [workshop.qmd](workshop.qmd) file is the file I use to compile the practical. Qmd stands for Quarto markdown. It allows code and ordinary text to be interleaved to produce well-formatted reports including webpages. Right-click on the link and choose Save-As to download. You will be able to open the Qmd file in RStudio. Alternatively, [View in Browser](https://github.com/3mmaRand/). Coding and thinking answers are marked with `#---CODING ANSWER---` and `#---THINKING ANSWER---`
+The [workshop.qmd](workshop.qmd) file is the file I use to compile the
+practical. Qmd stands for Quarto markdown. It allows code and ordinary
+text to be interleaved to produce well-formatted reports including
+webpages. Right-click on the link and choose Save-As to download. You
+will be able to open the Qmd file in RStudio. Alternatively, [View in
+Browser](https://github.com/3mmaRand/). Coding and thinking answers are
+marked with `#---CODING ANSWER---` and `#---THINKING ANSWER---`
 
-Pages made with R [@R-core], Quarto [@allaire2022], `knitr` [@knitr], `kableExtra` [@kableExtra]
+Pages made with R [@R-core], Quarto [@allaire2022], `knitr` [@knitr],
+`kableExtra` [@kableExtra]
 
 # References
diff --git a/omics/week-3/study_before_workshop.qmd b/omics/week-3/study_before_workshop.qmd
index abe473d..5a0534f 100644
--- a/omics/week-3/study_before_workshop.qmd
+++ b/omics/week-3/study_before_workshop.qmd
@@ -2,7 +2,13 @@
 title: "Independent Study to prepare for workshop"
 subtitle: "Omics 1: Hello data!"
 author: "Emma Rand"
-format: revealjs
+format: 
+  revealjs:
+    footer: "🔗 [About Omics 1: Hello data!](https://3mmarand.github.io/BIO00088H-data/omics/week-3/overview.html)"
+    slide-number: true
+    chalkboard: true
+    code-link: true
+    code-line-numbers: false
 bibliography: ../../references.bib
 editor: 
   markdown: 
diff --git a/references.bib b/references.bib
index d8a02c5..8a4039c 100644
--- a/references.bib
+++ b/references.bib
@@ -230,3 +230,52 @@ @article{markowetz2015
 	doi = {10.1186/s13059-015-0850-7},
 	url = {http://dx.doi.org/10.1186/s13059-015-0850-7}
 }
+
+@book{bryan,
+	title = {What They Forgot to Teach You About R},
+	author = {Bryan, Jennifer and Hester, Jim and Pileggi, Shannon and Aja, E. David},
+	url = {https://rstats.wtf/}
+}
+
+@article{sandve2013,
+	title = {Ten simple rules for reproducible computational research},
+	author = {Sandve, Geir Kjetil and Nekrutenko, Anton and Taylor, James and Hovig, Eivind},
+	year = {2013},
+	month = {10},
+	date = {2013-10},
+	journal = {PLoS Comput. Biol.},
+	pages = {e1003285},
+	volume = {9},
+	number = {10},
+	doi = {10.1371/journal.pcbi.1003285},
+	url = {http://dx.doi.org/10.1371/journal.pcbi.1003285}
+}
+
+@article{wilson2017,
+	title = {Good enough practices in scientific computing},
+	author = {Wilson, Greg and Bryan, Jennifer and Cranston, Karen and Kitzes, Justin and Nederbragt, Lex and Teal, Tracy K},
+	year = {2017},
+	month = {06},
+	date = {2017-06},
+	journal = {PLoS Comput. Biol.},
+	pages = {e1005510},
+	volume = {13},
+	number = {6},
+	doi = {10.1371/journal.pcbi.1005510},
+	url = {http://dx.doi.org/10.1371/journal.pcbi.1005510}
+}
+
+@article{bryan2018,
+	title = {Excuse Me, Do You Have a Moment to Talk About Version Control?},
+	author = {Bryan, Jennifer},
+	year = {2018},
+	month = {01},
+	date = {2018-01-02},
+	journal = {Am. Stat.},
+	pages = {20--27},
+	volume = {72},
+	number = {1},
+	doi = {10.1080/00031305.2017.1399928},
+	url = {https://doi.org/10.1080/00031305.2017.1399928},
+	note = {Publisher: Taylor & Francis}
+}
diff --git a/renv.lock b/renv.lock
index 521576c..4f6962a 100644
--- a/renv.lock
+++ b/renv.lock
@@ -97,13 +97,13 @@
     },
     "askpass": {
       "Package": "askpass",
-      "Version": "1.1",
+      "Version": "1.2.0",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
         "sys"
       ],
-      "Hash": "e8a22846fff485f0be3770c2da758713"
+      "Hash": "cad6cf7f1d5f6e906700b9d3e718c796"
     },
     "backports": {
       "Package": "backports",
@@ -184,7 +184,7 @@
     },
     "bslib": {
       "Package": "bslib",
-      "Version": "0.5.0",
+      "Version": "0.5.1",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
@@ -200,7 +200,7 @@
         "rlang",
         "sass"
       ],
-      "Hash": "1b117970533deb6d4e992c1b34e9d905"
+      "Hash": "283015ddfbb9d7bf15ea9f0b5698f0d9"
     },
     "cachem": {
       "Package": "cachem",
@@ -303,10 +303,13 @@
     },
     "cpp11": {
       "Package": "cpp11",
-      "Version": "0.4.4",
+      "Version": "0.4.6",
       "Source": "Repository",
       "Repository": "RSPM",
-      "Hash": "3f7d8664d7324406cd10cd650ad85e5f"
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "707fae4bbf73697ec8d85f9d7076c061"
     },
     "crayon": {
       "Package": "crayon",
@@ -322,13 +325,13 @@
     },
     "curl": {
       "Package": "curl",
-      "Version": "5.0.1",
+      "Version": "5.0.2",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
         "R"
       ],
-      "Hash": "2118af9cb164c8d2dddc7b89eaf732d9"
+      "Hash": "511bacbfa153a15251166b463b4da4f9"
     },
     "data.table": {
       "Package": "data.table",
@@ -343,7 +346,7 @@
     },
     "dbplyr": {
       "Package": "dbplyr",
-      "Version": "2.3.3",
+      "Version": "2.3.4",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
@@ -367,7 +370,7 @@
         "vctrs",
         "withr"
       ],
-      "Hash": "d6fd1b1440c1cacc6623aaa4e9fe352b"
+      "Hash": "63534894354af6b2587b7aa518a5193a"
     },
     "desc": {
       "Package": "desc",
@@ -396,7 +399,7 @@
     },
     "dplyr": {
       "Package": "dplyr",
-      "Version": "1.1.2",
+      "Version": "1.1.3",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
@@ -415,7 +418,7 @@
         "utils",
         "vctrs"
       ],
-      "Hash": "dea6970ff715ca541c387de363ff405e"
+      "Hash": "e85ffbebaad5f70e1a2e2ef4302b4949"
     },
     "dtplyr": {
       "Package": "dtplyr",
@@ -486,7 +489,7 @@
     },
     "fontawesome": {
       "Package": "fontawesome",
-      "Version": "0.5.1",
+      "Version": "0.5.2",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
@@ -494,7 +497,7 @@
         "htmltools",
         "rlang"
       ],
-      "Hash": "1e22b8cabbad1eae951a75e9f8b52378"
+      "Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d"
     },
     "forcats": {
       "Package": "forcats",
@@ -514,18 +517,18 @@
     },
     "fs": {
       "Package": "fs",
-      "Version": "1.6.2",
+      "Version": "1.6.3",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
         "R",
         "methods"
       ],
-      "Hash": "94af08e0aa9675a16fadbb3aaaa90d2a"
+      "Hash": "47b5f30c720c23999b913a1a635cf0bb"
     },
     "gargle": {
       "Package": "gargle",
-      "Version": "1.5.1",
+      "Version": "1.5.2",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
@@ -543,7 +546,7 @@
         "utils",
         "withr"
       ],
-      "Hash": "d3a3cb2fefea5b3d4f8e0ea33c948406"
+      "Hash": "fc0b272e5847c58cd5da9b20eedbd026"
     },
     "generics": {
       "Package": "generics",
@@ -558,7 +561,7 @@
     },
     "ggplot2": {
       "Package": "ggplot2",
-      "Version": "3.4.2",
+      "Version": "3.4.3",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
@@ -579,7 +582,7 @@
         "vctrs",
         "withr"
       ],
-      "Hash": "3a147ee02e85a8941aad9909f1b43b7b"
+      "Hash": "85846544c596e71f8f46483ab165da33"
     },
     "glue": {
       "Package": "glue",
@@ -647,7 +650,7 @@
     },
     "gtable": {
       "Package": "gtable",
-      "Version": "0.3.3",
+      "Version": "0.3.4",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
@@ -658,7 +661,7 @@
         "lifecycle",
         "rlang"
       ],
-      "Hash": "b44addadb528a0d227794121c00572a0"
+      "Hash": "b29cf3031f49b04ab9c852c912547eef"
     },
     "haven": {
       "Package": "haven",
@@ -708,7 +711,7 @@
     },
     "htmltools": {
       "Package": "htmltools",
-      "Version": "0.5.5",
+      "Version": "0.5.6",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
@@ -721,11 +724,11 @@
         "rlang",
         "utils"
       ],
-      "Hash": "ba0240784ad50a62165058a27459304a"
+      "Hash": "a2326a66919a3311f7fbb1e3bf568283"
     },
     "httr": {
       "Package": "httr",
-      "Version": "1.4.6",
+      "Version": "1.4.7",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
@@ -736,7 +739,7 @@
         "mime",
         "openssl"
       ],
-      "Hash": "7e5e3cbd2a7bc07880c94e22348fb661"
+      "Hash": "ac107251d9d9fd72f0ca8049988f1d7f"
     },
     "ids": {
       "Package": "ids",
@@ -792,7 +795,7 @@
     },
     "knitr": {
       "Package": "knitr",
-      "Version": "1.43",
+      "Version": "1.44",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
@@ -804,18 +807,18 @@
         "xfun",
         "yaml"
       ],
-      "Hash": "9775eb076713f627c07ce41d8199d8f6"
+      "Hash": "60885b9f746c9dfaef110d070b5f7dc0"
     },
     "labeling": {
       "Package": "labeling",
-      "Version": "0.4.2",
+      "Version": "0.4.3",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
         "graphics",
         "stats"
       ],
-      "Hash": "3d5108641f47470611a32d0bdf357a72"
+      "Hash": "b64ec208ac5bc1852b285f665d6368b3"
     },
     "lattice": {
       "Package": "lattice",
@@ -847,7 +850,7 @@
     },
     "lubridate": {
       "Package": "lubridate",
-      "Version": "1.9.2",
+      "Version": "1.9.3",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
@@ -856,7 +859,7 @@
         "methods",
         "timechange"
       ],
-      "Hash": "e25f18436e3efd42c7c590a1c4c15390"
+      "Hash": "680ad542fbcf801442c83a6ac5a2126c"
     },
     "magrittr": {
       "Package": "magrittr",
@@ -951,13 +954,13 @@
     },
     "openssl": {
       "Package": "openssl",
-      "Version": "2.1.0",
+      "Version": "2.1.1",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
         "askpass"
       ],
-      "Hash": "273a6bb4a9844c296a459d2176673270"
+      "Hash": "2a0dc8c6adfb6f032e4d4af82d258ab5"
     },
     "pillar": {
       "Package": "pillar",
@@ -988,10 +991,13 @@
     },
     "prettyunits": {
       "Package": "prettyunits",
-      "Version": "1.1.1",
+      "Version": "1.2.0",
       "Source": "Repository",
       "Repository": "RSPM",
-      "Hash": "95ef9167b75dde9d2ccc3c7528393e7e"
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "6b01fc98b1e86c4f705ce9dcfd2f57c7"
     },
     "processx": {
       "Package": "processx",
@@ -1032,7 +1038,7 @@
     },
     "purrr": {
       "Package": "purrr",
-      "Version": "1.0.1",
+      "Version": "1.0.2",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
@@ -1043,7 +1049,7 @@
         "rlang",
         "vctrs"
       ],
-      "Hash": "d71c815267c640f17ddbf7f16144b4bb"
+      "Hash": "1cba04a4e9414bdefc9dcaa99649a8dc"
     },
     "ragg": {
       "Package": "ragg",
@@ -1106,10 +1112,10 @@
     },
     "rematch": {
       "Package": "rematch",
-      "Version": "1.0.1",
+      "Version": "2.0.0",
       "Source": "Repository",
       "Repository": "RSPM",
-      "Hash": "c66b930d20bb6d858cd18e1cebcfae5c"
+      "Hash": "cbff1b666c6fa6d21202f07e2318d4f1"
     },
     "rematch2": {
       "Package": "rematch2",
@@ -1166,7 +1172,7 @@
     },
     "rmarkdown": {
       "Package": "rmarkdown",
-      "Version": "2.23",
+      "Version": "2.25",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
@@ -1186,7 +1192,7 @@
         "xfun",
         "yaml"
       ],
-      "Hash": "79f14e53725f28900d936f692bfdd69f"
+      "Hash": "d65e35823c817f09f4de424fcdfa812a"
     },
     "rprojroot": {
       "Package": "rprojroot",
@@ -1441,13 +1447,33 @@
     },
     "tinytex": {
       "Package": "tinytex",
-      "Version": "0.45",
+      "Version": "0.46",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
         "xfun"
       ],
-      "Hash": "e4e357f28c2edff493936b6cb30c3d65"
+      "Hash": "0c41a73214d982f539c56a7773c7afa5"
+    },
+    "tweetrmd": {
+      "Package": "tweetrmd",
+      "Version": "0.0.10",
+      "Source": "GitHub",
+      "Remotes": "rstudio/webshot2",
+      "RemoteType": "github",
+      "RemoteHost": "api.github.com",
+      "RemoteRepo": "tweetrmd",
+      "RemoteUsername": "gadenbuie",
+      "RemoteRef": "HEAD",
+      "RemoteSha": "c683b537a4a5234ee750fff234d21e4e9c201ba8",
+      "Requirements": [
+        "htmltools",
+        "httr",
+        "jsonlite",
+        "knitr",
+        "rmarkdown"
+      ],
+      "Hash": "b50c4fb0ff758a2d457f4e18c4c3b5b3"
     },
     "tzdb": {
       "Package": "tzdb",
@@ -1472,13 +1498,13 @@
     },
     "uuid": {
       "Package": "uuid",
-      "Version": "1.1-0",
+      "Version": "1.1-1",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
         "R"
       ],
-      "Hash": "f1cb46c157d080b729159d407be83496"
+      "Hash": "3d78edfb977a69fc7a0341bee25e163f"
     },
     "vctrs": {
       "Package": "vctrs",
@@ -1532,7 +1558,7 @@
     },
     "withr": {
       "Package": "withr",
-      "Version": "2.5.0",
+      "Version": "2.5.1",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
@@ -1541,18 +1567,18 @@
         "graphics",
         "stats"
       ],
-      "Hash": "c0e49a9760983e81e55cdd9be92e7182"
+      "Hash": "d77c6f74be05c33164e33fbc85540cae"
     },
     "xfun": {
       "Package": "xfun",
-      "Version": "0.39",
+      "Version": "0.40",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
         "stats",
         "tools"
       ],
-      "Hash": "8f56e9acb54fb525e66464d57ab58bcb"
+      "Hash": "be07d23211245fc7d4209f54c4e4ffc8"
     },
     "xml2": {
       "Package": "xml2",
diff --git a/styles.css b/styles.css
index c0be30b..d8c01a8 100644
--- a/styles.css
+++ b/styles.css
@@ -1,5 +1,6 @@
 /* css styles */
 
+
 .outputscroll {
 max-height: 400px;
 overflow-y: scroll;
diff --git a/update-notes.txt b/update-notes.txt
index 679e35a..c4a6289 100644
--- a/update-notes.txt
+++ b/update-notes.txt
@@ -31,3 +31,5 @@ Structure (Michael Plevin)
 
 🐭 Stem cell data:
 
+
+