Deploying to gh-pages from @ 620a195 🚀

core/core.html

@@ -289,8 +289,7 @@ <h2 class="anchored" data-anchor-id="week-1-core-1-organising-reproducible-data-
 </section>
 <section id="week-2-core-2-file-types-workflow-tips-and-other-tools" class="level2">
 <h2 class="anchored" data-anchor-id="week-2-core-2-file-types-workflow-tips-and-other-tools">Week 2 Core 2 File types, workflow tips and other tools</h2>
-<!-- Before  -->
-<!-- Apply to GitHub Global Campus as a student -->
+<p>This week we will consider File types, workflow tips and other tools. The independent study (~20 mins) reiterates the value of RStudio projects and shows you how you create them with usethis. You will also learn how to recognise and write cool 😎 code, not 😩 ugly code and code algorithmically. In the workshop we will examine some common biological data formats and discover some awesome short cuts to help you write cool 😎 code. You will also get a brief introduction to the command line and Google Colab.</p>
 <!-- After -->
 </section>
 <section id="week-6-core-3-reproducible-reporting" class="level2">

core/week-2/overview.html

@@ -267,7 +267,7 @@ <h1 class="title">Overview</h1>
 
 </header>
 
-<p>This week</p>
+<p>This week we will consider File types, workflow tips and other tools. The independent study reiterates the value of RStudio projects and shows you how you create them with <strong><code>usethis</code></strong>. You will also learn how to recognise and write cool 😎 code, not 😩 ugly code and code algorithmically. In the workshop we will examine some common biological data formats and discover some awesome short cuts to help you write cool 😎 code. You will also get a brief introduction to the command line and Google Colab.</p>
 <section id="learning-objectives" class="level3">
 <h3 class="anchored" data-anchor-id="learning-objectives">Learning objectives</h3>
 <p>The successful student will be able to:</p>

core/week-2/workshop.html

@@ -384,15 +384,15 @@ <h1 class="title">Workshop</h1>
 <div class="sourceCode cell-code" id="cb5"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" 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 140
--rw-r--r-- 1 runner docker 21116 Oct  2 16:27 chalkboard.json
-drwxr-xr-x 2 runner docker  4096 Oct  2 16:27 images
--rw-r--r-- 1 runner docker  1096 Oct  2 16:27 overview.qmd
--rw-r--r-- 1 runner docker   184 Oct  2 16:27 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 69876 Oct  2 16:34 study_before_workshop.html
--rw-r--r-- 1 runner docker  4807 Oct  2 16:27 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker 13029 Oct  2 16:27 study_before_workshop.qmd
--rw-r--r-- 1 runner docker  2396 Oct  2 16:27 workshop.qmd
--rw-r--r-- 1 runner docker  2400 Oct  2 16:34 workshop.rmarkdown</code></pre>
+-rw-r--r-- 1 runner docker 21116 Oct  2 16:46 chalkboard.json
+drwxr-xr-x 2 runner docker  4096 Oct  2 16:46 images
+-rw-r--r-- 1 runner docker  1597 Oct  2 16:46 overview.qmd
+-rw-r--r-- 1 runner docker   184 Oct  2 16:46 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker 69876 Oct  2 16:53 study_before_workshop.html
+-rw-r--r-- 1 runner docker  4807 Oct  2 16:46 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker 13029 Oct  2 16:46 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker  2396 Oct  2 16:46 workshop.qmd
+-rw-r--r-- 1 runner docker  2400 Oct  2 16:53 workshop.rmarkdown</code></pre>
 </div>
 </div>
 <div class="cell">

search.json

@@ -130,7 +130,7 @@
     "href": "core/week-2/workshop.html#rstudio-terminal",
     "title": "Workshop",
     "section": "RStudio terminal",
-    "text": "RStudio terminal\nThe 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\n\npwd\n\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2\n\n\n\nls\n\nchalkboard.json\nimages\noverview.qmd\nstudy_after_workshop.qmd\nstudy_before_workshop.html\nstudy_before_workshop.ipynb\nstudy_before_workshop.qmd\nworkshop.qmd\nworkshop.rmarkdown\n\n\n\nls -l\n\ntotal 140\n-rw-r--r-- 1 runner docker 21116 Oct  2 16:27 chalkboard.json\ndrwxr-xr-x 2 runner docker  4096 Oct  2 16:27 images\n-rw-r--r-- 1 runner docker  1096 Oct  2 16:27 overview.qmd\n-rw-r--r-- 1 runner docker   184 Oct  2 16:27 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 69876 Oct  2 16:34 study_before_workshop.html\n-rw-r--r-- 1 runner docker  4807 Oct  2 16:27 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13029 Oct  2 16:27 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker  2396 Oct  2 16:27 workshop.qmd\n-rw-r--r-- 1 runner docker  2400 Oct  2 16:34 workshop.rmarkdown\n\n\n\nls -F\n\nchalkboard.json\nimages/\noverview.qmd\nstudy_after_workshop.qmd\nstudy_before_workshop.html\nstudy_before_workshop.ipynb\nstudy_before_workshop.qmd\nworkshop.qmd\nworkshop.rmarkdown"
+    "text": "RStudio terminal\nThe 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\n\npwd\n\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2\n\n\n\nls\n\nchalkboard.json\nimages\noverview.qmd\nstudy_after_workshop.qmd\nstudy_before_workshop.html\nstudy_before_workshop.ipynb\nstudy_before_workshop.qmd\nworkshop.qmd\nworkshop.rmarkdown\n\n\n\nls -l\n\ntotal 140\n-rw-r--r-- 1 runner docker 21116 Oct  2 16:46 chalkboard.json\ndrwxr-xr-x 2 runner docker  4096 Oct  2 16:46 images\n-rw-r--r-- 1 runner docker  1597 Oct  2 16:46 overview.qmd\n-rw-r--r-- 1 runner docker   184 Oct  2 16:46 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 69876 Oct  2 16:53 study_before_workshop.html\n-rw-r--r-- 1 runner docker  4807 Oct  2 16:46 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13029 Oct  2 16:46 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker  2396 Oct  2 16:46 workshop.qmd\n-rw-r--r-- 1 runner docker  2400 Oct  2 16:53 workshop.rmarkdown\n\n\n\nls -F\n\nchalkboard.json\nimages/\noverview.qmd\nstudy_after_workshop.qmd\nstudy_before_workshop.html\nstudy_before_workshop.ipynb\nstudy_before_workshop.qmd\nworkshop.qmd\nworkshop.rmarkdown"
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@@ -172,7 +172,7 @@
     "href": "core/core.html",
     "title": "Core Data Analysis",
     "section": "",
-    "text": "There are three workshops taken by everyone on BIO00088H and BIO00070M. These are in weeks 1, 2 and 6. The first two cover some useful workflow tips and how to organise your analyses effectively so they are reproducible but you will also have the chance to revise material from stage 1 and 2.\nGood organisation is important because you will want to be able to set work aside for holidays and assessment periods and then restart easily. You will also be assessed on the organisation, reproducibility and transparency of your work.\n\n\nThis 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."
+    "text": "There are three workshops taken by everyone on BIO00088H and BIO00070M. These are in weeks 1, 2 and 6. The first two cover some useful workflow tips and how to organise your analyses effectively so they are reproducible but you will also have the chance to revise material from stage 1 and 2.\nGood organisation is important because you will want to be able to set work aside for holidays and assessment periods and then restart easily. You will also be assessed on the organisation, reproducibility and transparency of your work.\n\n\nThis 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.\n\n\n\nThis week we will consider File types, workflow tips and other tools. The independent study (~20 mins) reiterates the value of RStudio projects and shows you how you create them with usethis. You will also learn how to recognise and write cool 😎 code, not 😩 ugly code and code algorithmically. In the workshop we will examine some common biological data formats and discover some awesome short cuts to help you write cool 😎 code. You will also get a brief introduction to the command line and Google Colab."
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     "objectID": "core/core.html#week-1-core-1-organising-reproducible-data-analyses",
@@ -181,6 +181,13 @@
     "section": "",
     "text": "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."
   },
+  {
+    "objectID": "core/core.html#week-2-core-2-file-types-workflow-tips-and-other-tools",
+    "href": "core/core.html#week-2-core-2-file-types-workflow-tips-and-other-tools",
+    "title": "Core Data Analysis",
+    "section": "",
+    "text": "This week we will consider File types, workflow tips and other tools. The independent study (~20 mins) reiterates the value of RStudio projects and shows you how you create them with usethis. You will also learn how to recognise and write cool 😎 code, not 😩 ugly code and code algorithmically. In the workshop we will examine some common biological data formats and discover some awesome short cuts to help you write cool 😎 code. You will also get a brief introduction to the command line and Google Colab."
+  },
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     "href": "omics/week-3/study_after_workshop.html",
@@ -627,7 +634,7 @@
     "href": "core/week-2/overview.html",
     "title": "Overview",
     "section": "",
-    "text": "This week\n\nLearning objectives\nThe successful student will be able to:\n\nexplain why RStudio are useful/essential and be able to use the usethis package\nwrite cool 😎 code not 😩 ugly code\nexplain the value of code which expresses the structure of the problem/solution.\ndescribe some common file types for biological data\nuse some useful shortcuts to help write cool 😎 code\nknow what the command line is and how to use it for simple tasks\nuse Google colab to run code\nrecognise some of the differences between R and Python\n\n\n\nInstructions\n\nPrepare 20 mins reading on RStudio Projects revisited, formatting code and coding algorithmically\nWorkshop\n\n💬 Types of biological data files\n🪄 Workflow tips and shortcuts\n💻 The command line\n💻 Google colab\n💻 Python\n\nConsolidate\n\n💻 not sure yet :)"
+    "text": "This week we will consider File types, workflow tips and other tools. The independent study reiterates the value of RStudio projects and shows you how you create them with usethis. You will also learn how to recognise and write cool 😎 code, not 😩 ugly code and code algorithmically. In the workshop we will examine some common biological data formats and discover some awesome short cuts to help you write cool 😎 code. You will also get a brief introduction to the command line and Google Colab.\n\nLearning objectives\nThe successful student will be able to:\n\nexplain why RStudio are useful/essential and be able to use the usethis package\nwrite cool 😎 code not 😩 ugly code\nexplain the value of code which expresses the structure of the problem/solution.\ndescribe some common file types for biological data\nuse some useful shortcuts to help write cool 😎 code\nknow what the command line is and how to use it for simple tasks\nuse Google colab to run code\nrecognise some of the differences between R and Python\n\n\n\nInstructions\n\nPrepare 20 mins reading on RStudio Projects revisited, formatting code and coding algorithmically\nWorkshop\n\n💬 Types of biological data files\n🪄 Workflow tips and shortcuts\n💻 The command line\n💻 Google colab\n💻 Python\n\nConsolidate\n\n💻 not sure yet :)"
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